QCvis report
26 February 2021
This is an automatically-produced report from shinyQC. The analyzed data
contains 630 features and 88 samples.
1 Tab: Samples
1.1 Histogram
Use the settings
Categorical variable =name.
1.2 Mosaic
The mosaic plot was not called within the shiny application. Use default settings.
Use the settings
Categorical variable 1 =name andCategorical variable 2 =name.
2 Tab: Measured Values
2.1 Barplot for samples
2.2 Histogram Features
The ‘Histogram Features’ plot was not called within the shiny application. Use default settings.
Use the settings
Binwidth =1.
2.3 Histogram Features along variable
The ‘Histogram Features along variable’ plot was not called within the shiny application. Use default settings.
Use the settings
Variable for stratification =name andBinwidth =1.
2.4 UpSet
The ‘Upset’ plot was not called within the shiny application. Use default settings.
Use the settings
Variable for stratification =name.
3 Tab: Missing Values
3.1 Barplot for samples
3.2 Histogram Features
The ‘Histogram Features’ plot was not called within the shiny application. Use default settings.
Use the settings
Binwidth =1.
3.3 Histogram Features along variable
The ‘Histogram Features along variable’ plot was not called within the shiny application. Use default settings.
Use the settings
Variable for stratification =name andBinwidth =1.
3.4 UpSet
The ‘Upset’ plot was not called within the shiny application. Use default settings.
Use the settings
Variable for stratification =name.
4 Tab: Intensities
4.1 Boxplot/Violin plot
Use the settings
Display log2 values? =FALSE andType of display =FALSE.
4.2 Trend/drift
Use the settings
Select variable =,
Select level to highlight =,Select data input =raw,Select aggregation =sum,Select smoothing method =loess, andSelect variable to order samples =.
4.3 Coefficient of variation
4.4 Mean-sd plot
4.5 MA plot
The ‘MA plot’ was not called within the shiny application. Use default settings.
Use the settings
group =all,
plot =all,Data set for the MA plot =raw, andlines =FALSE.
4.6 ECDF
The ‘ECDF’ plot was not called within the shiny application. Use default settings.
Use the settings
Data set for the ECDF plot =raw,
Sample =1_Plasma_4C_0_C1, andgroup =all.
4.7 Distance matrix
The ‘Distance matrix’ plots were not called within the shiny application. Use default settings.
Use the settings
annotation =name anddistance method =euclidean.
5 Tab: Dimension Reduction
5.1 PCA
The ‘PCA’ plot was not called within the shiny application. Use default settings.
Use the settings
x-axis =PC1,y-axis =PC2,scale =TRUE,center =TRUE, andHighlight =none.
5.2 PCoA
The ‘PCoA’ plot was not called within the shiny application. Use default settings.
Use the settings
x-axis =Axis.1,y-axis =Axis.2,Distance measure =euclidean, andHighlight =none.
5.3 NMDS
The ‘NMDS’ plot was not called within the shiny application. Use default settings.
Use the settings
x-axis =MDS1,y-axis =MDS2,Distance measure =euclidean, andHighlight =none.
## Run 0 stress 9.8761e-05
## Run 1 stress 9.754276e-05
## ... New best solution
## ... Procrustes: rmse 2.886935e-05 max resid 0.0001422001
## ... Similar to previous best
## Run 2 stress 9.86572e-05
## ... Procrustes: rmse 1.153469e-05 max resid 3.100026e-05
## ... Similar to previous best
## Run 3 stress 9.594461e-05
## ... New best solution
## ... Procrustes: rmse 0.0001095138 max resid 0.0003442642
## ... Similar to previous best
## Run 4 stress 9.597091e-05
## ... Procrustes: rmse 5.576928e-05 max resid 0.0003360568
## ... Similar to previous best
## Run 5 stress 9.972704e-05
## ... Procrustes: rmse 0.0001139659 max resid 0.0003331439
## ... Similar to previous best
## Run 6 stress 0.0001031675
## ... Procrustes: rmse 0.0001307271 max resid 0.0003813627
## ... Similar to previous best
## Run 7 stress 9.736016e-05
## ... Procrustes: rmse 0.0001224382 max resid 0.0003583916
## ... Similar to previous best
## Run 8 stress 9.986547e-05
## ... Procrustes: rmse 0.0001047054 max resid 0.0003592288
## ... Similar to previous best
## Run 9 stress 9.13122e-05
## ... New best solution
## ... Procrustes: rmse 6.509991e-05 max resid 0.0002655749
## ... Similar to previous best
## Run 10 stress 9.823867e-05
## ... Procrustes: rmse 0.0001081686 max resid 0.000279633
## ... Similar to previous best
## Run 11 stress 9.778621e-05
## ... Procrustes: rmse 6.981572e-05 max resid 0.000270329
## ... Similar to previous best
## Run 12 stress 9.798048e-05
## ... Procrustes: rmse 0.0001144515 max resid 0.0004243048
## ... Similar to previous best
## Run 13 stress 9.98246e-05
## ... Procrustes: rmse 8.444349e-05 max resid 0.0004618941
## ... Similar to previous best
## Run 14 stress 9.955774e-05
## ... Procrustes: rmse 0.0001026056 max resid 0.0004400828
## ... Similar to previous best
## Run 15 stress 9.889913e-05
## ... Procrustes: rmse 7.846163e-05 max resid 0.000279398
## ... Similar to previous best
## Run 16 stress 9.731138e-05
## ... Procrustes: rmse 8.529584e-05 max resid 0.0002259614
## ... Similar to previous best
## Run 17 stress 9.410327e-05
## ... Procrustes: rmse 6.725978e-05 max resid 0.0002614167
## ... Similar to previous best
## Run 18 stress 9.432414e-05
## ... Procrustes: rmse 7.68446e-05 max resid 0.000506901
## ... Similar to previous best
## Run 19 stress 9.893589e-05
## ... Procrustes: rmse 8.42744e-05 max resid 0.0002169461
## ... Similar to previous best
## Run 20 stress 9.898755e-05
## ... Procrustes: rmse 8.362943e-05 max resid 0.000181727
## ... Similar to previous best
## *** Solution reached5.4 tSNE
The ‘tSNE’ plot was not called within the shiny application. Use default settings.
Use the settings
x-axis =X1,y-axis =X2,Perplexity =10,Number of iterations =1000,Number of retained dimensions in intial PCA =10,Output dimensionality =3,scale =TRUE,center =TRUE, andHighlight =none.
5.5 UMAP
The ‘UMAP’ plot was not called within the shiny application. Use default settings.
Use the settings
x-axis =X1,y-axis =X2,Minimum distance =0.1,Number of neighbors =15,Spread =1, andHighlight =none.